Polarizable force field for RNA based on the classical drude oscillator

Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field

(2018) Mingjun Yang et al.   CARBOHYDRATE RESEARCH

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator

(2018) Fang-Yu Lin et al.   Journal of Chemical Theory and Computation

Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases

(2017) Changsheng Zhang et al.   Journal of Chemical Theory and Computation

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

(2017) Asaminew H. Aytenfisu et al.   Journal of Chemical Theory and Computation

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics

(2017) Justin A. Lemkul et al.   Journal of Chemical Theory and Computation

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

(2017) Justin A. Lemkul et al.   Journal of Chemical Theory and Computation

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

(2017) Hui Li et al.   Journal of Chemical Theory and Computation

Physics-based all-atom modeling of RNA energetics and structure

(2017) Louis G. Smith et al.   Wiley Interdisciplinary Reviews-RNA

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

(2016) Petra Kührová et al.   Journal of Chemical Theory and Computation

Assessing the Current State of Amber Force Field Modifications for DNA

(2016) Rodrigo Galindo-Murillo et al.   Journal of Chemical Theory and Computation

Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model

(2016) Justin A. Lemkul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

(2016) Sandro Bottaro et al.   Journal of Physical Chemistry Letters

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

(2016) Leonardo Darré et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Control of the negative IREStrans-acting factor KHSRP by ubiquitination

(2016) Yu-An Kung et al.   NUCLEIC ACIDS RESEARCH

How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

(2016) Jiří Šponer et al.   Wiley Interdisciplinary Reviews-RNA

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

(2015) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

(2015) Hui Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

(2015) Madhurima Jana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

(2015) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

(2015) Heping Zheng et al.   NUCLEIC ACIDS RESEARCH

Mighty tiny

(2015) Kathleen B. Hall   RNA

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

(2015) Christina Bergonzo et al.   RNA

All-atom polarizable force field for DNA based on the classical drude oscillator model

(2014) Alexey Savelyev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

(2014) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator

(2014) Dhilon S. Patel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

(2014) Justin A. Lemkul et al.   Journal of Physical Chemistry Letters

Differential Impact of the Monovalent Ions Li+, Na+, K+, and Rb+ on DNA Conformational Properties

(2014) Alexey Savelyev et al.   Journal of Physical Chemistry Letters

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

(2014) Yihan Shao et al.   MOLECULAR PHYSICS

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Impact of Geometry Optimization on Base–Base Stacking Interaction Energies in the Canonical A- and B-Forms of DNA

(2013) Ashley Ringer McDonald et al.   JOURNAL OF PHYSICAL CHEMISTRY A

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

(2013) Janamejaya Chowdhary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Intrinsic Contribution of the 2′-Hydroxyl to RNA Conformational Heterogeneity

(2012) Elizabeth J. Denning et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine

(2010) Ilyas Yildirim et al.   Journal of Chemical Theory and Computation

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

(2010) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model

(2010) Christopher M. Baker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Finding 3D motifs in ribosomal RNA structures

(2009) A. Apostolico et al.   NUCLEIC ACIDS RESEARCH

High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA

(2009) Senada Nozinovic et al.   NUCLEIC ACIDS RESEARCH

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

(2009) Pedro E. M. Lopes et al.   THEORETICAL CHEMISTRY ACCOUNTS

RNA Folding: Thermodynamic and Molecular Descriptions of the Roles of Ions

(2008) David E. Draper   BIOPHYSICAL JOURNAL

Automated conformational energy fitting for force-field development

(2008) Olgun Guvench et al.   JOURNAL OF MOLECULAR MODELING

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

(2008) J. S. Richardson et al.   RNA